My Pono had a few too, so I used a drafting metal eraser shield similar to this:
http://www.duall.com/store/product/104739.104739/eraser-shield-template.html
masking tape the neck first, then carefully tape or hold the shield down firmly with the fret end poking thru a hole or slot, and then used a small jewelers file to dress the protruding fret(s) flush.
I have no idea how its to be properly done, but this worked for me. :shaka: